Currently Supported Importer Formats
The OMERO.importer uses the LOCI bio-formats library to support a number of formats. Please note however that we try to extensively test each file format before we add it to the importer, so our success depends on how much test data we have.
As always, contributions of sample data will help to ensure that the OMERO.importer accurately supports a wide range of formats, and any contributions you may wish to make are always welcome by contacting us at:
| Format | Extentions | Beta 2.1 |
Beta 2.2 |
Beta 2.3 |
Beta 2.3.1 |
Beta 3.0 |
Comments |
|---|---|---|---|---|---|---|---|
| BioRad | .pic | Yes | Yes | Yes | Yes | Yes | |
| - multi-plane "stitched" files | -- | -- | -- | -- | -- | Bio-format's BioRadReader currently does not stitch multiple .pic files into one "combined" image. | |
| - annotated ROI images | -- | -- | -- | -- | -- | There has been a report that annotated .pic files with regions of interest do not import and we are currently investigating this. | |
| Bitmap1 | .bmp | -- | Yes | Yes | Yes | Yes | We are currently working to fully support this format. |
| - Single-plane Combined Color | -- | Yes | Yes | Yes | Yes | ||
| - Compressed | -- | -- | -- | -- | -- | ||
| - Multi-plane Color Images | -- | -- | -- | -- | -- | ||
| DeltaVision | .dv, *.r3d, *.r3d_d3d | Yes | Yes | Yes | Yes | Yes | |
| Digital Imaging and Communications in Medicine | .dicom, .dic, .dcm | -- | Yes | Yes | Yes | Yes | Compressed dicoms import incorrectly and show up as garbled images in OMERO.insight. However, we are currely working to fix this problem. |
| - Compressed | -- | -- | -- | -- | -- | ||
| - Images with Negative Pixel Values | -- | Yes | Yes | Yes | Yes | ||
| Graphics Interchange Format1 | .gif | -- | Yes | Yes | Yes | Yes | |
| Image Cytometry Standard | .ics, ids | -- | -- | -- | Yes | Yes | |
| Imaris Raw Images | .ims | -- | Yes | Yes | Yes | Yes | |
| - 5.0 format | -- | Yes | Yes | Yes | Yes | ||
| - 5.5 format | -- | Yes | Yes | Yes | Yes | ||
| Improvision Tiff | .tif | -- | Yes | Yes | Yes | Yes | |
| Joint Photographic Experts Group12 | .jpeg, .jpg | -- | Yes | Yes | Yes | Yes | Lossless JPEG support is available via a native library extension. |
| Leica "lei" Format | .lei | Yes | Yes | Yes | Yes | Yes | |
| Leica Image Format | .lif | Yes | Yes | Yes | Yes | Yes | |
| Metamorph | .stk | Yes | Yes | Yes | Yes | Yes | |
| Nikon NIS-Elements2 | .nd2 | -- | -- | Yes | Yes | Yes | ND2 images based on the Lossless JPEG standard require a linked static library. |
| Olympus FluoView FV1000 | .oib, .oif | -- | -- | -- | Yes | Yes | |
| Openlab Raw | .raw | -- | Yes | Yes | Yes | Yes | |
| Openlab LIFF | .liff | -- | Yes | Yes | Yes | Yes | |
| OME-XML | .ome | -- | -- | -- | -- | Yes | |
| OME-TIFF | .ome.tiff | -- | -- | -- | -- | Yes | |
| PerkinElmer UltraView | .tif, .2, .3, etc | -- | -- | -- | Yes | Yes | |
| PICT (Machintosh Picture) | .pict | -- | -- | Yes | Yes | Yes | |
| Portable Gray Map1 | .pgm | -- | Yes | Yes | Yes | Yes | |
| Portable Network Graphic1 | .png | -- | Yes | Yes | Yes | Yes | |
| Prairie Technologies TIFF | .png | -- | -- | Yes | Yes | Yes | |
| Tagged Image File Format1 | .tif, .tiff | Yes | Yes | Yes | Yes | Yes | This is a very open standard, so expect a few variant types to be unsupported. We do however do extensive tiff testing so the format is generally well supported. |
| - OME Tiff format | -- | -- | -- | -- | -- | ||
| Visitech XYS | .xys | Yes | Yes | Yes | Yes | Yes | The Visitech importer does not fully support all Visitech metadata included in the accompanying html file. |
| Zeiss LSM | .lsm | Yes | Yes | Yes | Yes | Yes | |
| Zeiss AxioVision | .zvi | -- | -- | -- | Yes | Yes | |
1. Since this format contains no metadata, the importer will use default values for the pixel size and channel meta data.
2. Please read http://trac.openmicroscopy.org.uk/omero/wiki/LosslessJPEG for information on installing the Lossless JPEG static libraries.
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